Added lidar2dems superbuild module, modified dockerfile, configure.sh…

… to install lidar2dems deps

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "modules/lidar2dems"]
-	path = modules/lidar2dems
-	url = https://github.com/pierotofy/lidar2dems

Dockerfile

@@ -19,7 +19,7 @@ jhead liblas-bin python-matplotlib libatlas-base-dev libgmp-dev libmpfr-dev swig
 RUN apt-get remove libdc1394-22-dev
 RUN pip install --upgrade pip
 RUN pip install setuptools
-RUN pip install -U PyYAML exifread gpxpy xmltodict catkin-pkg appsettings https://github.com/Applied-GeoSolutions/gippy/archive/v0.3.9.tar.gz
+RUN pip install -U PyYAML exifread gpxpy xmltodict catkin-pkg appsettings https://github.com/pierotofy/gippy/archive/v0.3.9.tar.gz
 
 ENV PYTHONPATH="$PYTHONPATH:/code/SuperBuild/install/lib/python2.7/dist-packages"
 ENV PYTHONPATH="$PYTHONPATH:/code/SuperBuild/src/opensfm"
@@ -49,12 +49,6 @@ COPY VERSION /code/VERSION
 
 RUN cd SuperBuild && mkdir build && cd build && cmake  .. && make -j$(nproc)     && cd ../.. && mkdir build && cd build && cmake .. && make -j$(nproc)
 
-# Update and initialize git submodules
-RUN git submodule update --init
-
-# Setup lidar2dems
-RUN CPLUS_INCLUDE_PATH=/usr/include/gdal C_INCLUDE_PATH=/usr/include/gdal /code/modules/lidar2dems/setup.py install && ln -s /code/SuperBuild/build/pdal/bin/pdal /usr/bin/pdal
-
 RUN apt-get -y remove libgl1-mesa-dri git cmake python-pip build-essential
 RUN apt-get install -y libvtk5-dev
 

SuperBuild/CMakeLists.txt

@@ -114,6 +114,7 @@ set(custom_libs OpenGV
 				Ecto
 				PDAL
 				MvsTexturing
+				Lidar2dems
 )
 
 # Dependencies of the SLAM module

SuperBuild/cmake/External-Lidar2dems.cmake

@@ -0,0 +1,25 @@
+set(_proj_name lidar2dems)
+set(_SB_BINARY_DIR "${SB_BINARY_DIR}/${_proj_name}")
+
+ExternalProject_Add(${_proj_name}
+  PREFIX            ${_SB_BINARY_DIR}
+  TMP_DIR           ${_SB_BINARY_DIR}/tmp
+  STAMP_DIR         ${_SB_BINARY_DIR}/stamp
+  #--Download step--------------
+  DOWNLOAD_DIR      ${SB_DOWNLOAD_DIR}/${_proj_name}
+  URL               https://github.com/pierotofy/lidar2dems/archive/master.zip
+  URL_MD5           6cfe2d081cda1680e6e98a9925651b03
+  #--Update/Patch step----------
+  UPDATE_COMMAND    ""
+  #--Configure step-------------
+  SOURCE_DIR        ${SB_SOURCE_DIR}/${_proj_name}
+  CONFIGURE_COMMAND ""
+  #--Build step-----------------
+  BUILD_COMMAND     ""
+  #--Install step---------------
+  INSTALL_COMMAND   "${SB_SOURCE_DIR}/${_proj_name}/install.sh" 
+  #--Output logging-------------
+  LOG_DOWNLOAD      OFF
+  LOG_CONFIGURE     OFF
+  LOG_BUILD         OFF
+)

configure.sh

@@ -72,7 +72,7 @@ install() {
                         appsettings
 
     echo "Installing CGAL dependencies"
-    sudo apt-get install libgmp-dev libmpfr-dev
+    sudo apt-get install -y -qq libgmp-dev libmpfr-dev
 
     echo "Installing Ecto Dependencies"
     sudo pip install -U catkin-pkg
@@ -92,17 +92,8 @@ install() {
                          libboost-log-dev  \
                          libxslt-dev
 
-    echo "Updating and initializing git submodules"
-    git submodule update --init
+    sudo pip install -U https://github.com/pierotofy/gippy/archive/v0.3.9.tar.gz
 
-    echo "Installing lidar2dems"
-    cd ${RUNPATH}/modules/lidar2dems
-    CPLUS_INCLUDE_PATH=/usr/include/gdal C_INCLUDE_PATH=/usr/include/gdal ./setup.py install
-
-    if [ ! -f /usr/bin/pdal ]; then
-        ln -s ${RUNPATH}/SuperBuild/build/pdal/bin/pdal /usr/bin/pdal
-    fi
-
     echo "Compiling SuperBuild"
     cd ${RUNPATH}/SuperBuild
     mkdir -p build && cd build

opendm/types.py

@@ -196,7 +196,7 @@ def convert_to_las(self, _file, _file_out, json_file):
         system.run('{bin}/pdal pipeline -i {json} --readers.ply.filename={f_in} '
                    '--writers.las.filename={f_out}'.format(**kwargs))
 
-    def convert_to_dem(self, _file, _file_out, pdalJSON, sample_radius, gdal_res, gdal_radius):
+    def convert_to_dem(self, _file, _file_out, sample_radius, gdal_res, gdal_radius):
         # Check if exists f_in
         if not io.file_exists(_file):
             log.ODM_ERROR('LAS file does not exist')
@@ -208,36 +208,9 @@ def convert_to_dem(self, _file, _file_out, pdalJSON, sample_radius, gdal_res, gd
             'sample_radius': sample_radius,
             'gdal_res': gdal_res,
             'gdal_radius': gdal_radius,
-            'f_out': _file_out,
-            'json': pdalJSON
+            'f_out': _file_out
         }
 
-        pipelineJSON = '{{' \
-                       '    "pipeline":[' \
-                       '        "input.las",' \
-                       '    {{' \
-                       '        "type":"filters.sample",' \
-                       '        "radius":"{sample_radius}"' \
-                       '    }},' \
-                       '    {{' \
-                       '        "type":"filters.pmf"' \
-                       '    }},' \
-                       '    {{' \
-                       '      "type":"filters.range",' \
-                       '      "limits":"Classification[2:2]"' \
-                       '    }},' \
-                       '    {{' \
-                       '        "resolution": {gdal_res},' \
-                       '        "radius": {gdal_radius},' \
-                       '        "output_type":"idw",' \
-                       '        "filename":"outputfile.tif"' \
-                       '    }}' \
-                       '    ]' \
-                       '}}'.format(**kwargs)
-
-        with open(pdalJSON, 'w') as f:
-            f.write(pipelineJSON)
-
         system.run('{bin}/pdal pipeline {json} --readers.las.filename={f_in} '
                    '--writers.gdal.filename={f_out}'.format(**kwargs))
 
@@ -454,8 +427,6 @@ def __init__(self, root_path, images_path):
             self.odm_georeferencing, 'odm_georeferenced_model.las')
         self.odm_georeferencing_dem = io.join_paths(
             self.odm_georeferencing, 'odm_georeferencing_model_dem.tif')
-        self.odm_georeferencing_dem_json = io.join_paths(
-            self.odm_georeferencing, 'dem.json')
 
         # odm_orthophoto
         self.odm_orthophoto_file = io.join_paths(self.odm_orthophoto, 'odm_orthophoto.png')

scripts/odm_georeferencing.py

@@ -179,7 +179,6 @@ def find(file, dir):
                 if args.dem:
                     demcreated = geo_ref.convert_to_dem(tree.odm_georeferencing_model_las,
                                                         tree.odm_georeferencing_dem,
-                                                        tree.odm_georeferencing_dem_json,
                                                         self.params.sample_radius,
                                                         self.params.gdal_res,
                                                         self.params.gdal_radius)